Up to the time of secularization, the Mission continued to be one of the most prosperous.  Jesus Vallejo was the administrator for secularization, and in 1837 he and Padre Gonzalez Rubio made an inventory which gave a total of over $155,000, when all debts were paid.  Even now for awhile it seemed to prosper, and not until 1840 did the decline set in.

In accordance with Micheltorena’s decree of March 29, 1843, San Jose was restored to the temporal control of the padres, who entered with good-will and zest into the labor of saving what they could out of the wreck.  Under Pico’s decree of 1845 the Mission was inventoried, but the document cannot now be found, nor a copy of it.  The population was reported as 400 in 1842, and it is supposed that possibly 250 still lived at the Mission in 1845.  On May 5, 1846, Pico sold all the property to Andres Pico and J.B.  Alvarado for $12,000, but the sale never went into effect.

Mission San Jose de Guadalupe and the pueblo of the same name are not, as so many people, even residents of California, think, one and the same.  The pueblo of San Jose is now the modern city of that name, the home of the State Normal School, and the starting-point for Mount Hamilton.  But Mission San Jose is a small settlement, nearly twenty miles east and north, in the foothills overlooking the southeast end of San Francisco Bay.  The Mission church has entirely disappeared, an earthquake in 1868 having completed the ruin begun by the spoliation at the time of secularization.  A modern parish church has since been built upon the site.  Nothing of the original Mission now remains except a portion of the monastery.  The corridor is without arches, and is plain and unpretentious, the roof being composed of willows tied to the roughly hewn log rafters with rawhide.  Behind this is a beautiful old alameda of olives, at the upper end of which a modern orphanage, conducted by the Dominican Sisters, has been erected.  This avenue of olives is crossed by another one at right angles, and both were planted by the padres in the early days, as is evidenced by the age of the trees.  Doubtless many a procession of Indian neophytes has walked up and down here, even as I saw a procession of the orphans and their white-garbed guardians a short time ago.  The surrounding garden is kept up in as good style under the care of the sisters as it was in early days by the padres.

The orphanage was erected in 1884 by Archbishop Alemany as a seminary for young men who wished to study for the priesthood, but it was never very successful in this work.  For awhile it remained empty, then was offered to the Dominican Sisters as a boarding-school.  But as this undertaking did not pay, in 1891 Archbishop Riordan offered such terms as led the Mother General of the Dominican Sisters to purchase it as an orphanage, and as such it is now most successfully conducted.  There are at the present time about eighty children cared for by these sweet and gentle sisters of our Lord.